NGS course
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Welcome to this introductory course about NGS data analysis and visualization. During this course you will learn the basics of NGS data analysis and visualization in a Linux environment, current used software and best practices will be explained. This course is focused in NGS data alignment for both DNA and RNA (RNA-seq), variant calling, differential expression analysis and data visualization.

This is course is scheduled for a 3 days and assumes a very basic knowledge of NGS data analysis and Linux. All materials in this is course are free and open, feel free to reuse them as you want. All the data for the tutorials are available in our DropBox folder.


Day 1

During this first day we will start with an introduction to NGS technology and in the data preparation for their analysis. You will also learn the basics of the GNU/Linux shell introduction. At this point we are ready to start preparing and working with the data: Quality Control (QC) and NGS data alignment.


Introduction to NGS technologies

Very brief overview about NGS technologies and some concepts.

Introduction to GNU/Linux shell

Quality control for NGS raw data (FASTQ)

DNA and RNA-seq read alignment

Day 2

During the second day we will focus on Variant Calling and Data Visualization of DNA and RNA-seq alignments together with VCF files.

NGS data Visualization

Variant calling analysis

Variant annotation

Variant prioritization

Big Data analysis and visualization

Day 3

In the last day we will work on RNA-seq data analysis

Association studies

RNA-Seq data analysis

Functional analysis


This course is usually carried out by experienced researchers from CIPF, EMBL-EBI and University of Cambridge. You can ask any question to David Montaner (, Marta Bleda ( and Ignacio Medina (